B. Austin, Vibrios as causal agents of zoonoses, Veterinary Microbiology, vol.140, issue.3-4, pp.310-317, 2010.
DOI : 10.1016/j.vetmic.2009.03.015

URL : https://hal.archives-ouvertes.fr/hal-00556049

J. Castresana, Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis, Molecular Biology and Evolution, vol.17, issue.4, pp.540-552, 2000.
DOI : 10.1080/106351598261067

O. Cordero, H. Wildschutte, B. Kirkup, S. Proehl, L. Ngo et al., Ecological 544 populations of bacteria act as socially cohesive units of antibiotic production and resistance, p.545, 2012.

V. Daubin, M. Gouy, and G. Perriere, A Phylogenomic Approach to Bacterial Phylogeny: Evidence of a Core of Genes Sharing a Common History, Genome Research, vol.12, issue.7, pp.1080-1090, 2002.
DOI : 10.1101/gr.187002

URL : https://hal.archives-ouvertes.fr/hal-00427259

R. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004.
DOI : 10.1093/nar/gkh340

URL : https://academic.oup.com/nar/article-pdf/32/5/1792/7055030/gkh340.pdf

B. Finlay and S. Falkow, Common themes in microbial pathogenicity revisited, p.554, 1997.

C. Goarant, Y. Reynaud, D. Ansquer, S. De-decker, D. Saulnier et al., Molecular epidemiology of Vibrio nigripulchritudo, a pathogen of cultured penaeid shrimp (Litopenaeus stylirostris) in New Caledonia, Systematic and Applied Microbiology, vol.29, issue.7, pp.570-580, 2006.
DOI : 10.1016/j.syapm.2005.12.005

S. Guindon, J. Dufayard, V. Lefort, M. Anisimova, W. Hordijk et al., New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0, Systematic Biology, vol.174, issue.3, pp.307-321, 2010.
DOI : 10.1093/bioinformatics/17.4.383

URL : https://hal.archives-ouvertes.fr/lirmm-00511784

M. Hoffmann, S. Monday, M. Allard, E. Strain, P. Whittaker et al., Vibrio 569, 2012.

J. Huerta-cepas, J. Dopazo, and T. Gabaldon, ETE: a python Environment for Tree 573, 2010.
DOI : 10.1186/1471-2105-11-24

URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-11-24?site=bmcbioinformatics.biomedcentral.com

M. Hurst, T. Glare, and T. Jackson, Cloning Serratia entomophila antifeeding genes, p.576, 2004.

M. Hurst, S. Beard, T. Jackson, and S. Jones, Isolation and characterization of the 580, 2007.

S. Kroken, N. Glass, J. Taylor, O. Yoder, and B. Turgeon, Phylogenomic analysis of 583, 2003.

L. Roux, F. Binesse, J. Saulnier, D. Mazel, and D. , Construction of a Vibrio splendidus Mutant Lacking the Metalloprotease Gene vsm by Use of a Novel Counterselectable Suicide Vector, Applied and Environmental Microbiology, vol.73, issue.3, pp.777-784, 2007.
DOI : 10.1128/AEM.02147-06

L. Roux, F. Labreuche, Y. Davis, B. Iqbal, N. Mangenot et al., Virulence 591 of an emerging pathogenic lineage of Vibrio nigripulchritudo is dependent on two plasmids, Environmental microbiology, vol.13, pp.592-296, 2011.

M. Medema, K. Blin, P. Cimermancic, V. De-jager, P. Zakrzewski et al., 595 antiSMASH: rapid identification, annotation and analysis of secondary metabolite 596, 2011.

J. Nosanchuk and A. Casadevall, The contribution of melanin to microbial pathogenesis, Cellular Microbiology, vol.123, issue.4, p.600, 2003.
DOI : 10.7326/0003-4819-104-2-234

A. Pimenta, K. Racher, L. Jamieson, M. Blight, and I. Holland, Mutations in HlyD, part 603 of the type 1 translocator for hemolysin secretion, affect the folding of the secreted toxin, p.604, 2005.

F. Pond, I. Gibson, J. Lalucat, and R. Quackenbush, R-body-producing bacteria, p.607, 1989.

K. Raymann, L. Bobay, T. Doak, M. Lynch, and S. Gribaldo, A genomic survey of reb 610 homologs suggests widespread occurrence of R-bodies in proteobacteria, G3 (Bethesda), vol.3, pp.611-505, 2013.

F. Reen, S. Almagro-moreno, D. Ussery, and E. Boyd, The genomic code: inferring, p.614, 2006.
DOI : 10.1038/nrmicro1476

URL : http://orbit.dtu.dk/en/publications/the-genomic-code-inferring-vibrionaceae-niche-specialization(fcf2fb90-88ff-487f-abd2-c369b0939a46).html

Y. Reynaud, D. Saulnier, D. Mazel, C. Goarant, L. Roux et al., Correlation between 617 detection of a plasmid and high-level virulence of Vibrio nigripulchritudo, p.618, 2008.

T. Sakai, T. Hirae, K. Yuasa, T. Kamaishi, T. Matsuyama et al., Mass mortality 621 of cultured kuruma prawn Peneaus japonicus caused by Vibrio nigripulchritudo. Fish 622, Pathology, vol.42, pp.141-147, 2007.

K. Satchell, MARTX, multifunctional autoprocessing repeats-in-toxin toxins, p.625, 2007.

J. Staunton and K. Weissman, Polyketide biosynthesis: a millennium review, Natural Product Reports, vol.18, issue.4, 2001.
DOI : 10.1039/a909079g

F. Thompson, T. Iida, and J. Swings, Biodiversity of Vibrios, Microbiology and Molecular Biology Reviews, vol.68, issue.3, pp.635-403, 2004.
DOI : 10.1128/MMBR.68.3.403-431.2004

D. Vallenet, S. Engelen, D. Mornico, S. Cruveiller, L. Fleury et al., MicroScope: a platform for microbial genome annotation and comparative genomics, Database, vol.34, issue.suppl_1, p.21, 2009.
DOI : 10.1093/nar/gkj001

URL : https://academic.oup.com/database/article-pdf/doi/10.1093/database/bap021/16728594/bap021.pdf

N. Waterfield, B. Wren, and R. Ffrench-constant, Invertebrates as a source of emerging human pathogens, Nature Reviews Microbiology, vol.70, issue.10, pp.833-841, 2004.
DOI : 10.1016/S1438-4221(00)80024-7

R. Wozniak and M. Waldor, Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow, Nature Reviews Microbiology, vol.5, issue.8, pp.552-563, 2010.
DOI : 10.1128/jb.173.22.7136-7141.1991

J. Zaitseva, S. Jenewein, C. Oswald, T. Jumpertz, I. Holland et al., A molecular 648 understanding of the catalytic cycle of the nucleotide-binding domain of the ABC transporter 649, 2005.

D. Zerbino and E. Birney, Velvet: algorithms for de novo short read assembly using de 652, 2008.
DOI : 10.1101/gr.074492.107

URL : http://genome.cshlp.org/content/18/5/821.full.pdf

N. Ziemert, S. Podell, K. Penn, J. Badger, E. Allen et al., The natural product 655 domain seeker NaPDoS: a phylogeny based bioinformatic tool to classify secondary 656, 2012.